Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004764.1 Kokia drynarioides strain JFW-HI SEQ_118367, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 987

Length: 1645
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25


Found at i:413 original size:205 final size:205

Alignment explanation


    Indices: 60--579  Score: 713
    Period size: 205  Copynumber: 2.5  Consensus size: 205

         50 CCAACTCAGG

                                    *                                      * 
         60 GCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGT-GAAAC
          1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA-GGTCGAAGC

                            **                                      *     *  
        124 AATAAAAGGTTAGCTTATTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGGTA
         65 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTAATGAGATA

                        *                                        **          
        189 CAGAGAAGCAGATTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGGAGAAAACCAA
        130 CAGAGAAGCAGACTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAAAAGAAAACCAA

                      *
        254 ATCAAACCCAT
        195 ATCAAACCCAC

                     *                                 *          *          
        265 GCTCGATGTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACA-TCGAGAAGTAGGTCGAAGC
          1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACT-GAGAAGCAGGTCGAAGC

                                   *                        *                
        329 AATAAAAGGTTAGCTTCCTGATGCGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATA
         65 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTAATGAGATA

                     *                ** *  *                           *    
        394 CAGAGAAG-TGAACTGAAACAAACGATGCGGTTATCTTCCTGATGAGATACTGAAAAGAAGACCA
        130 CAGAGAAGCAG-ACTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAAAAGAAAACCA

                   *    
        458 AATCAAATCCAC
        194 AATCAAACCCAC

                   *            *                                          * 
        470 GCTCGATATGAGCAAATCTTGGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTA
          1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA

                                  * *    * *      *      
        535 ATAAAACGGTTAGCTTCCTGATAAAATACGGGGAAGTGAACCAAA
         66 ATAAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAA

        580 ACCAAATTCC


Statistics
Matches: 276,  Mismatches: 34, Indels: 9
        0.87            0.11        0.03

Matches are distributed among these distances:
 204    5  0.02
 205  238  0.86
 206   33  0.12

ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22


Consensus pattern (205 bp):   
GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTAATGAGATAC
AGAGAAGCAGACTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAAAAGAAAACCAAA
TCAAACCCAC

Found at i:995 original size:6 final size:6

Alignment explanation


    Indices: 981--1061  Score: 73
    Period size: 6  Copynumber: 14.0  Consensus size: 6

        971 TTCAATTTAT

                       *       *                                    
        981 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA

                        *                       *     
       1027 TTT-AA TTTAAT TTTAAA TTT-AA TTTCAAA ATTAAA
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA

       1062 AGTCCAAAAA


Statistics
Matches: 61,  Mismatches: 7, Indels: 14
        0.74            0.09        0.17

Matches are distributed among these distances:
   4    2  0.03
   5   15  0.25
   6   37  0.61
   7    7  0.11

ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52


Consensus pattern (6 bp):   
TTTAAA

Found at i:997 original size:17 final size:17

Alignment explanation


    Indices: 974--1061  Score: 104
    Period size: 17  Copynumber: 5.1  Consensus size: 17

        964 CCCCTTTTTC

                             
        974 AATTTATTTTAAATTTA
          1 AATTTATTTTAAATTTA

            *                
        991 GATTTATTTTAAATTTA
          1 AATTTATTTTAAATTTA

                *  *         
       1008 AATTAATCTTAAATTTA
          1 AATTTATTTTAAATTTA

                  *     *    
       1025 AATTTAATTTAATTTTA
          1 AATTTATTTTAAATTTA

                      *   *   
       1042 AATTTAATTTCAAAATTA
          1 AATTT-ATTTTAAATTTA

              
       1060 AA
          1 AA

       1062 AGTCCAAAAA


Statistics
Matches: 58,  Mismatches: 12, Indels: 1
        0.82            0.17        0.01

Matches are distributed among these distances:
  17   48  0.83
  18   10  0.17

ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52


Consensus pattern (17 bp):   
AATTTATTTTAAATTTA

Found at i:1007 original size:23 final size:22

Alignment explanation


    Indices: 981--1048  Score: 74
    Period size: 23  Copynumber: 3.2  Consensus size: 22

        971 TTCAATTTAT

                                   
        981 TTTAAATTTAGATTTATTTTAAA
          1 TTTAAATTTA-ATTTATTTTAAA

                            *     
       1004 TTTAAA-TT-A---ATCTTAAA
          1 TTTAAATTTAATTTATTTTAAA

                                   
       1021 TTTAAATTTAATTTAATTTTAAA
          1 TTTAAATTTAATTT-ATTTTAAA

                 
       1044 TTTAA
          1 TTTAA

       1049 TTTCAAAATT


Statistics
Matches: 37,  Mismatches: 2, Indels: 12
        0.73            0.04        0.24

Matches are distributed among these distances:
  17   13  0.35
  18    2  0.05
  19    1  0.03
  20    1  0.03
  22    2  0.05
  23   18  0.49

ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54


Consensus pattern (22 bp):   
TTTAAATTTAATTTATTTTAAA
Done.